Since updating to Mountain Lion on my iMac, I have found that on two occasions, Lightroom 4.1 seems to eject the wrong disk after import. I get a warning that a disk was not ejected properly and, when I look at the Finder, I see the CF card is still 'in' and one of my externals is ejected. It is missing in Disk Utility as well so I have to power it off/on to get it to reconnect.

I've had issues with that particular external in the past (connected via FW400 off a FW800 drive) but it's always been tempermental in getting an initial connection to the Mac. Once connected it always stayed so.

Though I would see if anyone had thoughts. If it came to it, do you think a 'reinstall' of LR would be helpful? Does this require removing all traces of the program first? I'm hesitant to do that as my catalog currently has 75,000 photos though...